Using MongoDB with Apache Tomcat, searching for Pubmed articles
The current post continues the previous one titled "
MongoDB and NCBI pubmed: Inserting, searching and updating. My notebook.".
Here I've used the Java API for MongoDB/BSON in Apache Tomcat, the java servlet container to search and display some pubmed papers stored in mongo via a web interface. At the end the result looks like this:
The servlet
The servlet uses the JAVA API for mongo.- An instance of Mongo is created and it connects to the mongodb server
- We obtain an object DB from the server for the database 'pubmed'
- we get an object DBCollection from the database
- If the user provided a valid pmid, the new query is created:BasicDBObject query=new BasicDBObject("_id",Long.parseLong(pmid))and it is used to search the collectionBObject article=collection.findOne(query);
- If the article was found, it was injected in the request and forwarded to the JSP named 'article.jsp'
File: src/WEB-INF/src/fr/inserm/umr915/biomongo/BioMongoServlet.java
package fr.inserm.umr915.biomongo;
import java.io.IOException;
import javax.servlet.ServletConfig;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import com.mongodb.BasicDBObject;
import com.mongodb.DB;
import com.mongodb.DBCollection;
import com.mongodb.DBObject;
import com.mongodb.Mongo;
import com.mongodb.ServerAddress;
@SuppressWarnings("serial")
public class BioMongoServlet extends HttpServlet
{
/** mongodb host */
private String mongoHost=ServerAddress.defaultHost();
/** mongodb port */
private int mongoPort=ServerAddress.defaultPort();
@Override
public void init(ServletConfig config) throws ServletException {
super.init(config);
String param=config.getInitParameter("mongo.port");
if(param!=null) this.mongoPort=Integer.parseInt(param);
param=config.getInitParameter("mongo.host");
if(param!=null) this.mongoHost=param;
}
@Override
protected void service(HttpServletRequest req, HttpServletResponse res)
throws ServletException, IOException
{
Mongo mongo=null;
try {
//connect to mongo
mongo = new Mongo(this.mongoHost,this.mongoPort);
//get the database pubmed
DB database=mongo.getDB("pubmed");
if(database==null) throw new ServletException("canot get database");
//get the collection 'articles'
DBCollection col = database.getCollection("articles");
if(col==null) throw new ServletException("canot get collection");
//get the query parameter 'pmid'
String pmid=req.getParameter("pmid");
String jspPage="/WEB-INF/jsp/index.jsp";
//if pmid exist and looks like a number
if(pmid!=null && pmid.matches("[0-9]+"))
{
//find
DBObject article=col.findOne(new BasicDBObject("_id",Long.parseLong(pmid)));
if(article==null)
{
req.setAttribute("message", "Cannot find pmid:"+pmid);
}
else
{
jspPage="/WEB-INF/jsp/article.jsp";
req.setAttribute("article",article);
}
}
req.getRequestDispatcher(jspPage).forward(req, res);
}
catch(ServletException e)
{
throw e;
}
catch(IOException e)
{
throw e;
}
catch(Exception e)
{
throw new ServletException(e);
}
finally
{
//cleanup mongo
if(mongo!=null)
{
mongo.close();
}
mongo=null;
}
}
}
import java.io.IOException;
import javax.servlet.ServletConfig;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import com.mongodb.BasicDBObject;
import com.mongodb.DB;
import com.mongodb.DBCollection;
import com.mongodb.DBObject;
import com.mongodb.Mongo;
import com.mongodb.ServerAddress;
@SuppressWarnings("serial")
public class BioMongoServlet extends HttpServlet
{
/** mongodb host */
private String mongoHost=ServerAddress.defaultHost();
/** mongodb port */
private int mongoPort=ServerAddress.defaultPort();
@Override
public void init(ServletConfig config) throws ServletException {
super.init(config);
String param=config.getInitParameter("mongo.port");
if(param!=null) this.mongoPort=Integer.parseInt(param);
param=config.getInitParameter("mongo.host");
if(param!=null) this.mongoHost=param;
}
@Override
protected void service(HttpServletRequest req, HttpServletResponse res)
throws ServletException, IOException
{
Mongo mongo=null;
try {
//connect to mongo
mongo = new Mongo(this.mongoHost,this.mongoPort);
//get the database pubmed
DB database=mongo.getDB("pubmed");
if(database==null) throw new ServletException("canot get database");
//get the collection 'articles'
DBCollection col = database.getCollection("articles");
if(col==null) throw new ServletException("canot get collection");
//get the query parameter 'pmid'
String pmid=req.getParameter("pmid");
String jspPage="/WEB-INF/jsp/index.jsp";
//if pmid exist and looks like a number
if(pmid!=null && pmid.matches("[0-9]+"))
{
//find
DBObject article=col.findOne(new BasicDBObject("_id",Long.parseLong(pmid)));
if(article==null)
{
req.setAttribute("message", "Cannot find pmid:"+pmid);
}
else
{
jspPage="/WEB-INF/jsp/article.jsp";
req.setAttribute("article",article);
}
}
req.getRequestDispatcher(jspPage).forward(req, res);
}
catch(ServletException e)
{
throw e;
}
catch(IOException e)
{
throw e;
}
catch(Exception e)
{
throw new ServletException(e);
}
finally
{
//cleanup mongo
if(mongo!=null)
{
mongo.close();
}
mongo=null;
}
}
}
article.jsp
article.jsp displays the article. As this object is an instance of BasicDBObject (that is to say a Map and/or a List) it was very easy to use it with the JSP technology and the Java Standard Tag Library (JSTL).File: ./src/WEB-INF/jsp/article.jsp
<%@page contentType="text/html" %>
<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
<%@ taglib prefix="mongo" tagdir="/WEB-INF/tags" %>
<% out.clearBuffer(); %><html><head>
<title>PMID:<c:out value="${param['pmid']}" escapeXml="true"/></title>
</head>
<body>
<h1>PMID:<c:out value="${param['pmid']}" escapeXml="true"/></h1>
<h2><c:out value="${article.title}" escapeXml="true"/></h2>
<dl>
<dt>Date</dt><dd><mongo:dbobject object="${article.created}"/></dd>
<dt>Authors</dt><dd><ul><c:forEach var="author" items="${article.authors}">
<li>
<mongo:dbobject object="${author}"/>
</li>
</c:forEach></ul></dd>
<dt>Journal</dt><dd><mongo:dbobject object="${article.journal}"/></dd>
<dt>Mesh</dt><dd><ul><c:forEach var="term" items="${article.mesh}">
<li>
<c:out value="${term}" escapeXml="true"/>
</li>
</c:forEach></ul></dd>
</dl>
</body>
</html>
<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
<%@ taglib prefix="mongo" tagdir="/WEB-INF/tags" %>
<% out.clearBuffer(); %><html><head>
<title>PMID:<c:out value="${param['pmid']}" escapeXml="true"/></title>
</head>
<body>
<h1>PMID:<c:out value="${param['pmid']}" escapeXml="true"/></h1>
<h2><c:out value="${article.title}" escapeXml="true"/></h2>
<dl>
<dt>Date</dt><dd><mongo:dbobject object="${article.created}"/></dd>
<dt>Authors</dt><dd><ul><c:forEach var="author" items="${article.authors}">
<li>
<mongo:dbobject object="${author}"/>
</li>
</c:forEach></ul></dd>
<dt>Journal</dt><dd><mongo:dbobject object="${article.journal}"/></dd>
<dt>Mesh</dt><dd><ul><c:forEach var="term" items="${article.mesh}">
<li>
<c:out value="${term}" escapeXml="true"/>
</li>
</c:forEach></ul></dd>
</dl>
</body>
</html>
dbobject.tag
The previous JSP page calls a custom tag file <mongo:dbobject> which make a 'pretty display' of a BSON object by serializing it with com.mongodb.util.JSON.serialize(Object o)File: ./src/WEB-INF/tags/dbobject.tag
<%@ tag language="java" pageEncoding="UTF-8"%>
<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
<%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions" %>
<%@tag import="com.mongodb.util.JSON"%>
<%@tag import="com.mongodb.DBObject"%>
<%@attribute name="object" required="true" rtexprvalue="true" type="java.lang.Object"%>
<c:set var="bson"><%= JSON.serialize(this.object) %></c:set>
<div style="background-color:lightgray;"><c:out escapeXml="true" value="${bson}"/></div>
<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
<%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions" %>
<%@tag import="com.mongodb.util.JSON"%>
<%@tag import="com.mongodb.DBObject"%>
<%@attribute name="object" required="true" rtexprvalue="true" type="java.lang.Object"%>
<c:set var="bson"><%= JSON.serialize(this.object) %></c:set>
<div style="background-color:lightgray;"><c:out escapeXml="true" value="${bson}"/></div>
Other Files
index.jsp
a simple form for searching an article.File: ./src/WEB-INF/jsp/index.jsp
<%@page contentType="text/html" %>
<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
<% out.clearBuffer(); %><html><head>
<title>Search PMID</title>
</head>
<body>
<form method="GET" action="${pageContext.request.contextPath}/biomongo" >
<div style=" position:absolute;width:400px;height:100px;left:50%;top:50%;margin-left:-100px;margin-top:-50px;">
<c:if test="${not empty message}">
<div style="text-align:center; color:red;"><c:out value="${message}" escapeXml="true"/></div>
</c:if>
<input name="pmid"/><input type="submit"/>
</div>
</form></body>
</html>
<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
<% out.clearBuffer(); %><html><head>
<title>Search PMID</title>
</head>
<body>
<form method="GET" action="${pageContext.request.contextPath}/biomongo" >
<div style=" position:absolute;width:400px;height:100px;left:50%;top:50%;margin-left:-100px;margin-top:-50px;">
<c:if test="${not empty message}">
<div style="text-align:center; color:red;"><c:out value="${message}" escapeXml="true"/></div>
</c:if>
<input name="pmid"/><input type="submit"/>
</div>
</form></body>
</html>
web.xml
the deployement descriptor.File: ./src/WEB-INF/web.xml
<?xml version="1.0" encoding="UTF-8"?>
<web-app xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd"
version="2.5">
<description>Biomongo Servlet</description>
<display-name>Biomongo</display-name>
<servlet>
<display-name>Biomongo Servlet</display-name>
<servlet-name>biomongo</servlet-name>
<servlet-class>fr.inserm.umr915.biomongo.BioMongoServlet</servlet-class>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>biomongo</servlet-name>
<url-pattern>/biomongo</url-pattern>
</servlet-mapping>
<jsp-config>
<taglib>
<taglib-uri>http://java.sun.com/jstl/fmt</taglib-uri>
<taglib-location>/WEB-INF/tld/fmt.tld</taglib-location>
</taglib>
<taglib>
<taglib-uri>http://java.sun.com/jstl/core</taglib-uri>
<taglib-location>/WEB-INF/tld/c.tld</taglib-location>
</taglib>
<taglib>
<taglib-uri>http://java.sun.com/jstl/sql</taglib-uri>
<taglib-location>/WEB-INF/tld/sql.tld</taglib-location>
</taglib>
<taglib>
<taglib-uri>http://java.sun.com/jstl/x</taglib-uri>
<taglib-location>/WEB-INF/tld/x.tld</taglib-location>
</taglib>
<taglib>
<taglib-uri>http://java.sun.com/jstl/functions</taglib-uri>
<taglib-location>/WEB-INF/tld/fn.tld</taglib-location>
</taglib>
</jsp-config>
</web-app>
<web-app xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd"
version="2.5">
<description>Biomongo Servlet</description>
<display-name>Biomongo</display-name>
<servlet>
<display-name>Biomongo Servlet</display-name>
<servlet-name>biomongo</servlet-name>
<servlet-class>fr.inserm.umr915.biomongo.BioMongoServlet</servlet-class>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>biomongo</servlet-name>
<url-pattern>/biomongo</url-pattern>
</servlet-mapping>
<jsp-config>
<taglib>
<taglib-uri>http://java.sun.com/jstl/fmt</taglib-uri>
<taglib-location>/WEB-INF/tld/fmt.tld</taglib-location>
</taglib>
<taglib>
<taglib-uri>http://java.sun.com/jstl/core</taglib-uri>
<taglib-location>/WEB-INF/tld/c.tld</taglib-location>
</taglib>
<taglib>
<taglib-uri>http://java.sun.com/jstl/sql</taglib-uri>
<taglib-location>/WEB-INF/tld/sql.tld</taglib-location>
</taglib>
<taglib>
<taglib-uri>http://java.sun.com/jstl/x</taglib-uri>
<taglib-location>/WEB-INF/tld/x.tld</taglib-location>
</taglib>
<taglib>
<taglib-uri>http://java.sun.com/jstl/functions</taglib-uri>
<taglib-location>/WEB-INF/tld/fn.tld</taglib-location>
</taglib>
</jsp-config>
</web-app>
An ANT file for building the project
File: build.xml
<?xml version="1.0" encoding="UTF-8"?>
<project default="biomongo">
<property file="build.properties"/>
<property name="root.dir" value="."/>
<property file="${rootdir}/build.properties"/>
<path id="mongo.path">
<pathelement location="${mongodb.lib}"/>
</path>
<path id="servlet.path">
<pathelement location="${tomcat.servlet.api}"/>
<pathelement location="${tomcat.jsp.api}"/>
</path>
<target name="biomongo">
<property name="base.dir" value="${root.dir}/biomongo"/>
<mkdir dir="${base.dir}/src/WEB-INF/lib"/>
<mkdir dir="${base.dir}/src/WEB-INF/classes"/>
<copy todir="${base.dir}/src/WEB-INF/lib" includeEmptyDirs="false">
<fileset file="${mongodb.lib}"/>
<fileset dir="${taglib.dir}/lib" includes="*.jar"/>
</copy>
<copy todir="${base.dir}/src/WEB-INF/tld" includeEmptyDirs="false">
<fileset dir="${taglib.dir}/tld" includes="*.tld"/>
</copy>
<javac srcdir="${base.dir}/src/WEB-INF/src"
destdir="${base.dir}/src/WEB-INF/classes"
debug="true"
source="1.6"
target="1.6">
<classpath>
<path refid="mongo.path"/>
<path refid="servlet.path"/>
</classpath>
<sourcepath>
<pathelement location="${base.dir}/src/WEB-INF/src"/>
</sourcepath>
<include name="**/BioMongoServlet.java"/>
</javac>
<jar destfile="${tomcat.dir}/webapps/biomongo.war"
basedir="${base.dir}/src">
</jar>
</target>
</project>
<project default="biomongo">
<property file="build.properties"/>
<property name="root.dir" value="."/>
<property file="${rootdir}/build.properties"/>
<path id="mongo.path">
<pathelement location="${mongodb.lib}"/>
</path>
<path id="servlet.path">
<pathelement location="${tomcat.servlet.api}"/>
<pathelement location="${tomcat.jsp.api}"/>
</path>
<target name="biomongo">
<property name="base.dir" value="${root.dir}/biomongo"/>
<mkdir dir="${base.dir}/src/WEB-INF/lib"/>
<mkdir dir="${base.dir}/src/WEB-INF/classes"/>
<copy todir="${base.dir}/src/WEB-INF/lib" includeEmptyDirs="false">
<fileset file="${mongodb.lib}"/>
<fileset dir="${taglib.dir}/lib" includes="*.jar"/>
</copy>
<copy todir="${base.dir}/src/WEB-INF/tld" includeEmptyDirs="false">
<fileset dir="${taglib.dir}/tld" includes="*.tld"/>
</copy>
<javac srcdir="${base.dir}/src/WEB-INF/src"
destdir="${base.dir}/src/WEB-INF/classes"
debug="true"
source="1.6"
target="1.6">
<classpath>
<path refid="mongo.path"/>
<path refid="servlet.path"/>
</classpath>
<sourcepath>
<pathelement location="${base.dir}/src/WEB-INF/src"/>
</sourcepath>
<include name="**/BioMongoServlet.java"/>
</javac>
<jar destfile="${tomcat.dir}/webapps/biomongo.war"
basedir="${base.dir}/src">
</jar>
</target>
</project>
Result
That's it.
Pierre
